A machine-learning study has identified mammals that are potential sources for new coronaviruses.
The research from the University of Liverpool was supported by the Biotechnology and Biological Sciences Research Council and the Medical Research Council.
Coronavirus generation in animals
The study, published in Nature Communications, suggests the potential scale of novel coronavirus generation in wild and domestic animals is greater than thought.
Predicting which animals could be the source of a future coronavirus outbreak may guide approaches to reduce the risk of coronavirus emergence in animals and spill-over to human populations.
Dr Maya Wardeh from the University of Liverpool’s Institute of Infection, Veterinary and Ecological Sciences, said:
New coronaviruses can emerge when two different strains co-infect an animal, causing the viral genetic material to recombine.
Our understanding of how susceptible different mammals are to different coronaviruses has been limited, but such information could offer insights into where viral recombination might occur.
Machine learning and mammals
The researchers used a machine learning approach to predict relationships between 411 strains of coronavirus and 876 potential mammalian host species.
Dr Maya Wardeh said:
We approached the prediction problem as though it were a puzzle with many sides.
From the mammal side we looked at evolutionary factors of the hosts of each coronavirus – diet and habitat, for example. On the virus side we looked at the secondary structure, or physical shape, of the genome and its combinations. We also looked at the network linking known coronaviruses and their hosts, which led us to the last side of the puzzle: the complex connections that already exist between coronaviruses and mammals.
Once we identified 12 factors on the three sides of the puzzle, we quantified the using a confidence score and finally blended them together, using an ensemble algorithm, to produce our final predictions.
The team’s findings suggest that there are at least 11 times more associations between mammalian species and coronavirus strains than thought.
They also estimate that there are over 40 times more mammal species that can be infected with a diverse set of coronavirus strains than previously known.
Dr Marcus Blagrove, co-lead of the study, said:
Given that coronaviruses frequently undergo recombination when they co-infect a host, and that SARS-CoV-2 is highly infectious to humans, the most immediate threat to public health is recombination of other coronaviruses with SARS-CoV-2.
The researchers went on to identify hosts in which SARS-CoV-2 recombination could potentially occur. Their findings indicate there may be 30 times more host species than currently known.
Notable new predicted hosts include:
- the dormitory camel
- African green monkey
- the lesser Asiatic yellow bat.
The researchers highlighted the high-risk scenario of recombination occurring between the highly transmissible SARS-CoV-2 and the more deadly MERS-CoV. They identified 102 potential recombination hosts of the two viruses and recommend monitoring for this event.
Dr Blagrove concluded:
It is important to note that viral recombination is distinct from mutations. Recombination occurs over longer periods of time and can generate completely new strains or species. Our work can help target surveillance programmes to discover future strains before they spill-over to humans, giving us a head-start in combating them.
The researchers now plan to expand their model to include bird species and a species-level contact network to give a broader overview of potential coronavirus associations.
Last updated: 6 May 2021